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Vacek J, Zatloukalova M, Bartheldyova E, Reha D, Minofar B, Bednarova K, Renciuk D, Coufal J, Fojta M, Zadny J, Gessini A, Rossi B, Storch J, Kabelac M. Hexahelicene DNA-binding: Minor groove selectivity, semi-intercalation and chiral recognition. Int J Biol Macromol 2023; 250:125905. [PMID: 37487990 DOI: 10.1016/j.ijbiomac.2023.125905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
In this contribution, we focused on a fundamental study targeting the interaction of water-soluble [6]helicene derivative 1 (1-butyl-3-(2-methyl[6]helicenyl)-imidazolium bromide) with double-stranded (ds) DNA. A synthetic 30-base pair duplex, plasmid, chromosomal calf thymus and salmon DNA were investigated using electrochemistry, electrophoresis and spectroscopic tools supported by molecular dynamics (MD) and quantum mechanical approaches. Both experimental and theoretical work revealed the minor groove binding of 1 to the dsDNA. Both the positively charged imidazole ring and hydrophobic part of the side chain contributed to the accommodation of 1 into the dsDNA structure. Neither intercalation into the duplex DNA nor the stable binding of 1 to single-stranded DNA were found in topoisomerase relaxation experiments with structural components of 1, i.e. [6]helicene (2) and 1-butyl-3-methylimidazolium bromide (3), nor by theoretical calculations. Finally, the binding of optically pure enantiomers (P)-1 and (M)-1 was studied using circular dichroism spectroscopy, isothermal titration calorimetry and UV Resonance Raman (UVRR) methods. Using MD and quantum mechanical methods, minor groove and semi-intercalation were proposed for compound 1 as the predominant binding modes. From the UVRR findings, we also can conclude that 1 tends to preferentially interact with adenine and guanine residues in the structure of dsDNA.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic.
| | - Martina Zatloukalova
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | | | - David Reha
- IT4Innovations, VSB-Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Babak Minofar
- Department of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
| | - Klara Bednarova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jan Coufal
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jaroslav Zadny
- Institute of Chemical Process Fundamentals of the AS CR, v.v.i., Rozvojova 135, 165 02 Prague 6, Czech Republic
| | - Alessandro Gessini
- Elettra Sincrotrone Trieste S.C.p.A., S.S. 14 - Km 163.5, Basovizza, Trieste I-34149, Italy
| | - Barbara Rossi
- Elettra Sincrotrone Trieste S.C.p.A., S.S. 14 - Km 163.5, Basovizza, Trieste I-34149, Italy
| | - Jan Storch
- Institute of Chemical Process Fundamentals of the AS CR, v.v.i., Rozvojova 135, 165 02 Prague 6, Czech Republic.
| | - Martin Kabelac
- Department of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
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Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication. Int J Mol Sci 2020; 21:ijms21124504. [PMID: 32599919 PMCID: PMC7349988 DOI: 10.3390/ijms21124504] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Key DNA transactions, such as genome replication and transcription, rely on the speedy translocation of specialized protein complexes along a double-stranded, right-handed helical template. Physical tethering of these molecular machines during translocation, in conjunction with their internal architectural features, generates DNA topological strain in the form of template supercoiling. It is known that the build-up of transient excessive supercoiling poses severe threats to genome function and stability and that highly specialized enzymes—the topoisomerases (TOP)—have evolved to mitigate these threats. Furthermore, due to their intracellular abundance and fast supercoil relaxation rates, it is generally assumed that these enzymes are sufficient in coping with genome-wide bursts of excessive supercoiling. However, the recent discoveries of chromatin architectural factors that play important accessory functions have cast reasonable doubts on this concept. Here, we reviewed the background of these new findings and described emerging models of how these accessory factors contribute to supercoil homeostasis. We focused on DNA replication and the generation of positive (+) supercoiling in front of replisomes, where two accessory factors—GapR and HMGA2—from pro- and eukaryotic cells, respectively, appear to play important roles as sinks for excessive (+) supercoiling by employing a combination of supercoil constrainment and activation of topoisomerases. Looking forward, we expect that additional factors will be identified in the future as part of an expanding cellular repertoire to cope with bursts of topological strain. Furthermore, identifying antagonists that target these accessory factors and work synergistically with clinically relevant topoisomerase inhibitors could become an interesting novel strategy, leading to improved treatment outcomes.
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The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. Int J Mol Sci 2019; 20:ijms20225605. [PMID: 31717504 PMCID: PMC6888028 DOI: 10.3390/ijms20225605] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/29/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
The tumor suppressor functions of p53 and its roles in regulating the cell cycle, apoptosis, senescence, and metabolism are accomplished mainly by its interactions with DNA. p53 works as a transcription factor for a significant number of genes. Most p53 target genes contain so-called p53 response elements in their promoters, consisting of 20 bp long canonical consensus sequences. Compared to other transcription factors, which usually bind to one concrete and clearly defined DNA target, the p53 consensus sequence is not strict, but contains two repeats of a 5′RRRCWWGYYY3′ sequence; therefore it varies remarkably among target genes. Moreover, p53 binds also to DNA fragments that at least partially and often completely lack this consensus sequence. p53 also binds with high affinity to a variety of non-B DNA structures including Holliday junctions, cruciform structures, quadruplex DNA, triplex DNA, DNA loops, bulged DNA, and hemicatenane DNA. In this review, we summarize information of the interactions of p53 with various DNA targets and discuss the functional consequences of the rich world of p53 DNA binding targets for its complex regulatory functions.
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Dual redox labeling of DNA as a tool for electrochemical detection of p53 protein-DNA interactions. Anal Chim Acta 2019; 1050:123-131. [DOI: 10.1016/j.aca.2018.10.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
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5
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Dávila–Rodríguez M, Barolli JP, de Oliveira KM, Colina–Vegas L, da Silva Miranda F, Castellano EE, Von Poelhsitz G, Batista AA. Carbonyl–heterobimetallic Ru(II)/Fe(II)–complexes containing polypyridyl ligands: Synthesis, characterization, cellular viability assays and interactions with biomolecules. Arch Biochem Biophys 2018; 660:156-167. [DOI: 10.1016/j.abb.2018.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/18/2022]
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Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States. Sci Rep 2018; 8:6163. [PMID: 29670174 PMCID: PMC5906655 DOI: 10.1038/s41598-018-24499-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 01/03/2023] Open
Abstract
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.
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Brázda V, Coufal J. Recognition of Local DNA Structures by p53 Protein. Int J Mol Sci 2017; 18:ijms18020375. [PMID: 28208646 PMCID: PMC5343910 DOI: 10.3390/ijms18020375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/03/2017] [Indexed: 02/06/2023] Open
Abstract
p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
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8
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Zatloukalová M, Vavříková E, Pontinha ADR, Coufal J, Křen V, Fojta M, Ulrichová J, Oliveira-Brett AM, Vacek J. Flavonolignan Conjugates as DNA-binding Ligands and Topoisomerase I Inhibitors: Electrochemical and Electrophoretic Approaches. ELECTROANAL 2016. [DOI: 10.1002/elan.201600146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry; Faculty of Medicine and Dentistry; Palacký University; Hněvotínská 3 775 15 Olomouc Czech Republic
- Department of Chemistry; Faculty of Science and Technology; University of Coimbra; 3004-535 Coimbra Portugal
| | - Eva Vavříková
- Institute of Microbiology; Laboratory of Biotransformation; Czech Academy of Sciences; Vídeňská 1083 142 20 Prague Czech Republic
| | - Ana Dora Rodrigues Pontinha
- Department of Chemistry; Faculty of Science and Technology; University of Coimbra; 3004-535 Coimbra Portugal
| | - Jan Coufal
- Institute of Biophysics; Department of Biophysical Chemistry and Molecular Oncology; Czech Academy of Sciences; Královopolská 135 612 65 Brno Czech Republic
| | - Vladimír Křen
- Institute of Microbiology; Laboratory of Biotransformation; Czech Academy of Sciences; Vídeňská 1083 142 20 Prague Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics; Department of Biophysical Chemistry and Molecular Oncology; Czech Academy of Sciences; Královopolská 135 612 65 Brno Czech Republic
| | - Jitka Ulrichová
- Department of Medical Chemistry and Biochemistry; Faculty of Medicine and Dentistry; Palacký University; Hněvotínská 3 775 15 Olomouc Czech Republic
| | - Ana Maria Oliveira-Brett
- Department of Chemistry; Faculty of Science and Technology; University of Coimbra; 3004-535 Coimbra Portugal
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry; Faculty of Medicine and Dentistry; Palacký University; Hněvotínská 3 775 15 Olomouc Czech Republic
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9
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Congur G, Plucnara M, Erdem A, Fojta M. Detection of p53 Gene by Using Genomagnetic Assay Combined with Carbon Nanotube Modified Disposable Sensor Technology. ELECTROANAL 2015. [DOI: 10.1002/elan.201400731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Bowater RP, Cobb AM, Pivonkova H, Havran L, Fojta M. Biophysical and electrochemical studies of protein–nucleic acid interactions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1405-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Šebest P, Brázdová M, Fojta M, Pivoňková H. Differential salt-induced dissociation of the p53 protein complexes with circular and linear plasmid DNA substrates suggest involvement of a sliding mechanism. Int J Mol Sci 2015; 16:3163-77. [PMID: 25647416 PMCID: PMC4346886 DOI: 10.3390/ijms16023163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/26/2015] [Indexed: 01/30/2023] Open
Abstract
A study of the effects of salt conditions on the association and dissociation of wild type p53 with different ~3 kbp long plasmid DNA substrates (supercoiled, relaxed circular and linear, containing or lacking a specific p53 binding site, p53CON) using immunoprecipitation at magnetic beads is presented. Salt concentrations above 200 mM strongly affected association of the p53 protein to any plasmid DNA substrate. Strikingly different behavior was observed when dissociation of pre-formed p53-DNA complexes in increased salt concentrations was studied. While contribution from the p53CON to the stability of the p53-DNA complexes was detected between 100 and 170 mM KCl, p53 complexes with circular DNAs (but not linear) exhibited considerable resistance towards salt treatment for KCl concentrations as high as 2 M provided that the p53 basic C-terminal DNA binding site (CTDBS) was available for DNA binding. On the contrary, when the CTDBS was blocked by antibody used for immunoprecipitation, all p53-DNA complexes were completely dissociated from the p53 protein in KCl concentrations ≥200 mM under the same conditions. These observations suggest: (a) different ways for association and dissociation of the p53-DNA complexes in the presence of the CTDBS; and (b) a critical role for a sliding mechanism, mediated by the C-terminal domain, in the dissociation process.
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Affiliation(s)
- Peter Šebest
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno CZ-625 00, Czech Republic.
| | - Hana Pivoňková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
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12
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Němcová K, Sebest P, Havran L, Orság P, Fojta M, Pivoňková H. Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode. Anal Bioanal Chem 2014; 406:5843-52. [PMID: 25056872 DOI: 10.1007/s00216-014-7996-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 06/22/2014] [Accepted: 06/24/2014] [Indexed: 11/28/2022]
Abstract
In this paper, we present an electrochemical DNA-protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT20 tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed.
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Affiliation(s)
- Kateřina Němcová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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Preferential binding of hot spot mutant p53 proteins to supercoiled DNA in vitro and in cells. PLoS One 2013; 8:e59567. [PMID: 23555710 PMCID: PMC3608670 DOI: 10.1371/journal.pone.0059567] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 02/19/2013] [Indexed: 11/21/2022] Open
Abstract
Hot spot mutant p53 (mutp53) proteins exert oncogenic gain-of-function activities. Binding of mutp53 to DNA is assumed to be involved in mutp53-mediated repression or activation of several mutp53 target genes. To investigate the importance of DNA topology on mutp53-DNA recognition in vitro and in cells, we analyzed the interaction of seven hot spot mutp53 proteins with topologically different DNA substrates (supercoiled, linear and relaxed) containing and/or lacking mutp53 binding sites (mutp53BS) using a variety of electrophoresis and immunoprecipitation based techniques. All seven hot spot mutp53 proteins (R175H, G245S, R248W, R249S, R273C, R273H and R282W) were found to have retained the ability of wild-type p53 to preferentially bind circular DNA at native negative superhelix density, while linear or relaxed circular DNA was a poor substrate. The preference of mutp53 proteins for supercoiled DNA (supercoil-selective binding) was further substantiated by competition experiments with linear DNA or relaxed DNA in vitro and ex vivo. Using chromatin immunoprecipitation, the preferential binding of mutp53 to a sc mutp53BS was detected also in cells. Furthermore, we have shown by luciferase reporter assay that the DNA topology influences p53 regulation of BAX and MSP/MST1 promoters. Possible modes of mutp53 binding to topologically constrained DNA substrates and their biological consequences are discussed.
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Brázda V, Čechová J, Coufal J, Rumpel S, Jagelská EB. Superhelical DNA as a preferential binding target of 14-3-3γ protein. J Biomol Struct Dyn 2012; 30:371-8. [DOI: 10.1080/07391102.2012.682205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Jana Čechová
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Sigrun Rumpel
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, University Health Network , Toronto, Ontario, Canada, M5G 2C4
| | - Eva B. Jagelská
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
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Travelli C, Drago V, Maldi E, Kaludercic N, Galli U, Boldorini R, Di Lisa F, Tron GC, Canonico PL, Genazzani AA. Reciprocal potentiation of the antitumoral activities of FK866, an inhibitor of nicotinamide phosphoribosyltransferase, and etoposide or cisplatin in neuroblastoma cells. J Pharmacol Exp Ther 2011; 338:829-40. [PMID: 21685314 DOI: 10.1124/jpet.111.184630] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
NAD is an essential coenzyme involved in numerous metabolic pathways. Its principal role is in redox reactions, and as such it is not heavily "consumed" by cells. Yet a number of signaling pathways that bring about its consumption have recently emerged. This has brought about the hypothesis that the enzymes that lead to its biosynthesis may be targets for anticancer therapy. In particular, inhibition of the enzyme nicotinamide phosphoribosyl transferase has been shown to be an effective treatment in a number of preclinical studies, and two lead molecules [N-[4-(1-benzoyl-4-piperidinyl)butyl]-3-(3-pyridinyl)-2E-propenamide (FK866) and (E)-1-[6-(4-chlorophenoxy)hexyl]-2-cyano-3-(pyridin-4-yl)guanidine (CHS 828)] have now entered preclinical trials. Yet, the full potential of these drugs is still unclear. In the present study we have investigated the role of FK866 in neuroblastoma cell lines. We now confirm that FK866 alone in neuroblastoma cells induces autophagy, and its effects are potentiated by chloroquine and antagonized by 3-methyladenine or by down-regulating autophagy-related protein 7. Autophagy, in this model, seems to be crucial for FK866-induced cell death. On the other hand, a striking potentiation of the effects of cisplatin and etoposide is given by cotreatment of cells with ineffective concentrations of FK866 (1 nM). The effect of etoposide on DNA damage is potentiated by FK866 treatment, whereas the effect of FK866 on cytosolic NAD depletion is potentiated by etoposide. Even more strikingly, cotreatment with etoposide/cisplatin and FK866 unmasks an effect on mitochondrial NAD depletion.
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Affiliation(s)
- Cristina Travelli
- Department of Chemical, Food, Pharmaceutical, and Pharmacological Sciences, Università del Piemonte Orientale, Novara, Italy
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16
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Vacek J, Vrublová E, Kubala M, Janovská M, Fojta M, Šimková E, Stýskala J, Skopalová J, Hrbáč J, Ulrichová J. Oxidation of Sanguinarine and Its Dihydro-Derivative at a Pyrolytic Graphite Electrode Using Ex Situ Voltammetry. Study of the Interactions of the Alkaloids with DNA. ELECTROANAL 2011. [DOI: 10.1002/elan.201100028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Benes P, Knopfova L, Trcka F, Nemajerova A, Pinheiro D, Soucek K, Fojta M, Smarda J. Inhibition of topoisomerase IIα: Novel function of wedelolactone. Cancer Lett 2011; 303:29-38. [DOI: 10.1016/j.canlet.2011.01.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/21/2010] [Accepted: 01/03/2011] [Indexed: 11/26/2022]
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Lachapelle S, Gagné JP, Garand C, Desbiens M, Coulombe Y, Bohr VA, Hendzel MJ, Masson JY, Poirier GG, Lebel M. Proteome-wide identification of WRN-interacting proteins in untreated and nuclease-treated samples. J Proteome Res 2011; 10:1216-27. [PMID: 21210717 DOI: 10.1021/pr100990s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Werner syndrome (WS) is characterized by the premature onset of several age-associated pathologies. The protein defective in WS patients (WRN) is a helicase/exonuclease involved in DNA repair, replication, telomere maintenance, and transcription. Here, we present the results of a large-scale proteome analysis to determine protein partners of WRN. We expressed fluorescent tagged-WRN (eYFP-WRN) in human 293 embryonic kidney cells and detected interacting proteins by co-immunoprecipitation from cell extract. We identified by mass spectrometry 220 nuclear proteins that complexed with WRN. This number was reduced to 40 when broad-spectrum nucleases were added to the lysate. We consider these 40 proteins as directly interacting with WRN. Some of these proteins have previously been shown to interact with WRN, whereas most are new partners. Among the top 15 hits, we find the new interactors TMPO, HNRNPU, RPS3, RALY, RPS9 DDX21, and HNRNPM. These proteins are likely important components in understanding the function of WRN in preventing premature aging and deserve further investigation. We have confirmed endogenous WRN interaction with endogenous RPS3, a ribosomal protein with endonuclease activities involved in oxidative DNA damage recognition. Our results suggest that the use of nucleases during cell lysis severely restricts interacting protein partners and thus enhances specificity.
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Affiliation(s)
- Sophie Lachapelle
- Centre de Recherche en Cancérologie de l'Université Laval, Hôpital Hôtel-Dieu de Québec, Québec City, Québec, G1R 2J6, Canada
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Horáková P, Macíčková-Cahová H, Pivoňková H, Spaček J, Havran L, Hocek M, Fojta M. Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl transferase. Application in electrochemical DNA hybridization and protein-DNA binding assays. Org Biomol Chem 2011; 9:1366-71. [PMID: 21203615 DOI: 10.1039/c0ob00856g] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple approach to DNA tail-labelling using terminal deoxynucleotidyl transferase and modified deoxynucleoside triphosphates is presented. Amino- and nitrophenyl-modified dNTPs were found to be good substrates for this enzyme giving 3'-end stretches of different lengths depending on the nucleotide and concentration. 3-Nitrophenyl-7-deazaG was selected as the most useful label because its dNTP was efficiently incorporated by the transferase to form long tail-labels at any oligonucleotide. Accumulation of many nitrophenyl tags per oligonucleotide resulted in a considerable enhancement of voltammetric signals due to the nitro group reduction, thus improving the sensitivity of electrochemical detection of the tail-labelled probes. We demonstrate a perfect discrimination between complementary and non-complementary target DNAs sequences by tail-labelled hybridization probes as well as the ability of tumour suppressor p53 protein to recognize a specific binding site within tail-labelled DNA substrates, making the methodology useful in electrochemical DNA hybridization and DNA-protein interaction assays.
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Affiliation(s)
- Petra Horáková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ-612 65, Brno, Czech Republic
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Němcová K, Havran L, Šebest P, Brázdová M, Pivoňková H, Fojta M. A label-free electrochemical test for DNA-binding activities of tumor suppressor protein p53 using immunoprecipitation at magnetic beads. Anal Chim Acta 2010; 668:166-70. [DOI: 10.1016/j.aca.2010.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/02/2010] [Accepted: 04/07/2010] [Indexed: 01/27/2023]
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